Variant report

Variant	rs10191933
Chromosome Location	chr2:11273099-11273100
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr2:11272869-11273474	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr2:11272585-11273337	HepG2	liver:	n/a	chr2:11272908-11272921 chr2:11272905-11272924
3	GABPA	chr2:11272628-11273328	A549	lung:	n/a	n/a
4	NR3C1	chr2:11272714-11273622	A549	lung:	n/a	chr2:11273361-11273375 chr2:11273360-11273376 chr2:11273361-11273375 chr2:11273360-11273376 chr2:11273357-11273378 chr2:11273090-11273104 chr2:11273360-11273376 chr2:11273360-11273376 chr2:11273355-11273381 chr2:11273358-11273371
5	TCF12	chr2:11272715-11273346	A549	lung:	n/a	n/a
6	REST	chr2:11272590-11273463	A549	lung:	n/a	chr2:11273188-11273197
7	CEBPB	chr2:11272777-11273302	IMR90	lung:	n/a	n/a
8	ELF1	chr2:11272608-11273291	K562	blood:	n/a	n/a
9	SMC3	chr2:11272685-11273402	HepG2	liver:	n/a	chr2:11272906-11272920
10	MAZ	chr2:11272719-11273271	Hela-S3	cervix:	n/a	n/a
11	RCOR1	chr2:11272629-11273221	K562	blood:	n/a	n/a
12	MXI1	chr2:11272794-11273402	Hela-S3	cervix:	n/a	chr2:11273196-11273211
13	SMC3	chr2:11272698-11273286	GM12878	blood:	n/a	chr2:11272906-11272920
14	MAX	chr2:11272471-11273510	MCF-7	breast:	n/a	n/a
15	ELK1	chr2:11272764-11273207	GM12878	blood:	n/a	n/a
16	CTCF	chr2:11272712-11273102	ECC-1	luminal epithelium:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
17	RAD21	chr2:11272690-11273135	Hela-S3	cervix:	n/a	chr2:11272908-11272921 chr2:11272905-11272924
18	SP4	chr2:11272686-11273354	H1-hESC	embryonic stem cell:	n/a	chr2:11273008-11273024 chr2:11273067-11273083 chr2:11273170-11273186 chr2:11273014-11273025
19	CTCF	chr2:11272654-11273103	H1-hESC	embryonic stem cell:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
20	REST	chr2:11272683-11273399	PFSK-1	brain:	n/a	chr2:11273188-11273197
21	RCOR1	chr2:11272664-11273198	Hela-S3	cervix:	n/a	n/a
22	TBP	chr2:11272689-11273439	H1-hESC	embryonic stem cell:	n/a	n/a
23	MYC	chr2:11272781-11273265	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAX	chr2:11272659-11273257	A549	lung:	n/a	n/a
25	SIN3AK20	chr2:11272763-11273399	HepG2	liver:	n/a	n/a
26	ZNF143	chr2:11272716-11273165	GM12878	blood:	n/a	n/a
27	CTCF	chr2:11272677-11273113	H1-hESC	embryonic stem cell:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
28	MXI1	chr2:11272770-11273358	H1-hESC	embryonic stem cell:	n/a	chr2:11273196-11273211
29	MAX	chr2:11272720-11273296	A549	lung:	n/a	n/a
30	ZKSCAN1	chr2:11272774-11273282	Hela-S3	cervix:	n/a	n/a
31	ELF1	chr2:11272615-11273369	GM12878	blood:	n/a	n/a
32	RAD21	chr2:11272529-11273226	A549	lung:	n/a	chr2:11272908-11272921 chr2:11272905-11272924
33	IRF1	chr2:11272743-11273283	K562	blood:	n/a	chr2:11273236-11273250 chr2:11273237-11273248 chr2:11273236-11273249 chr2:11273236-11273250 chr2:11273238-11273249
34	STAT1	chr2:11272846-11273363	GM12878	blood:	n/a	chr2:11273017-11273029 chr2:11273011-11273023 chr2:11273013-11273025
35	SMC3	chr2:11272659-11273459	Hela-S3	cervix:	n/a	chr2:11272906-11272920
36	RFX5	chr2:11272757-11273292	Hela-S3	cervix:	n/a	chr2:11273197-11273212
37	POLR2A	chr2:11272999-11273117	H1-hESC	embryonic stem cell:	n/a	n/a
38	TCF12	chr2:11272592-11273269	ECC-1	luminal epithelium:	n/a	n/a
39	E2F4	chr2:11272753-11273261	GM12878	blood:	n/a	n/a
40	MAFK	chr2:11272821-11273262	K562	blood:	n/a	n/a
41	MAX	chr2:11272779-11273187	GM12878	blood:	n/a	n/a
42	MYC	chr2:11272736-11273179	K562	blood:	n/a	n/a
43	HCFC1	chr2:11272526-11273409	K562	blood:	n/a	n/a
44	MAZ	chr2:11272745-11273402	HepG2	liver:	n/a	n/a
45	ZNF384	chr2:11272773-11273312	K562	blood:	n/a	n/a
46	MYBL2	chr2:11272477-11274028	HepG2	liver:	n/a	n/a
47	JUND	chr2:11272693-11273325	K562	blood:	n/a	n/a
48	REST	chr2:11272680-11273320	A549	lung:	n/a	chr2:11273188-11273197
49	HDAC2	chr2:11272777-11273399	HepG2	liver:	n/a	chr2:11273176-11273195
50	YY1	chr2:11272642-11273312	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:11273075-11273125	GM12891	blood:	n/a
2	chr2:11273075-11273125	LNCaP	prostate:	n/a
3	chr2:11273075-11273125	SK-N-SH	brain:	n/a
4	chr2:11273075-11273125	H1-hESC	embryonic stem cell:	embryo
5	chr2:11273075-11273125	Caco-2	colon:	n/a
6	chr2:11273075-11273125	Hela-S3	cervix:	n/a
7	chr2:11273075-11273125	GM12878	blood:	n/a
8	chr2:11273075-11273125	IMR90	lung:	fetal
9	chr2:11273075-11273125	Jurkat	blood:	n/a
10	chr2:11273075-11273125	HEEpiC	esophagus:	n/a
11	chr2:11273075-11273125	SAEC	small airway:	n/a
12	chr2:11273075-11273125	AG04450	lung:	fetal
13	chr2:11273075-11273125	HRE	kidney:	n/a
14	chr2:11273075-11273125	A549	lung:	n/a
15	chr2:11273075-11273125	NT2-D1	testis:	n/a
16	chr2:11273075-11273125	AG10803	skin:	n/a
17	chr2:11273075-11273125	PrEC	prostate:	n/a
18	chr2:11273075-11273125	BJ	skin:	n/a
19	chr2:11273075-11273125	PANC-1	pancreas:	n/a
20	chr2:11273075-11273125	BE2_C	brain:	n/a
21	chr2:11273075-11273125	ovcar-3	ovarian:	n/a
22	chr2:11273075-11273125	AG04449	skin:	fetal
23	chr2:11273075-11273125	CMK	blood:	n/a
24	chr2:11273075-11273125	GM19239	blood:	n/a
25	chr2:11273075-11273125	HNPCEpiC	eye:	n/a
26	chr2:11273075-11273125	AG09309	skin:	n/a
27	chr2:11273075-11273125	T-47D	breast:	n/a
28	chr2:11273075-11273125	HCF	heart:	n/a
29	chr2:11273075-11273125	HEK293	kidney:	embryo
30	chr2:11273075-11273125	HL-60	blood:	n/a
31	chr2:11273075-11273125	SK-N-MC	brain:	n/a
32	chr2:11273075-11273125	ECC-1	luminal epithelium:	n/a
33	chr2:11273075-11273125	HUVEC	blood vessel:	n/a
34	chr2:11273075-11273125	ProgFib	skin:	n/a
35	chr2:11273075-11273125	AG09319	gingival:	n/a
36	chr2:11273075-11273125	HCPEpiC	choroid plexus:	n/a
37	chr2:11273075-11273125	SKMC	muscle:	n/a
38	chr2:11273075-11273125	HRPEpiC	eye:	n/a
39	chr2:11273075-11273125	HepG2	liver:	n/a
40	chr2:11273075-11273125	HCT-116	colon:	n/a
41	chr2:11273075-11273125	GM12892	blood:	n/a
42	chr2:11273075-11273125	K562	blood:	n/a
43	chr2:11273075-11273125	SK-N-SH_RA	brain:	n/a
44	chr2:11273075-11273125	GM06990	blood:	n/a
45	chr2:11273075-11273125	RPTEC	kidney:	n/a
46	chr2:11273075-11273125	PFSK-1	brain:	n/a
47	chr2:11273075-11273125	HCM	heart:	n/a
48	chr2:11273075-11273125	HAEpiC	amniotic membrane:	n/a
49	chr2:11273075-11273125	HRCEpiC	kidney:	n/a
50	chr2:11273075-11273125	AoSMC	blood vessel:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:11272046..11273363-chr2:11723821..11725006,6	K562	blood:
2	chr2:11272147..11274930-chr2:11671339..11675156,3	MCF-7	breast:
3	chr2:11271098..11275692-chr2:11293512..11297101,4	MCF-7	breast:
4	chr2:11273055..11275301-chr2:11293268..11296881,3	MCF-7	breast:
5	chr2:11273067..11276077-chr2:11294167..11297061,3	K562	blood:
6	chr2:11269728..11273923-chr2:11678087..11684060,5	MCF-7	breast:
7	chr2:10972589..10973103-chr2:11272836..11273401,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145063	TF binding region
C2orf50	TF binding region
C2orf50	CpG island
ENSG00000145063	CpG island
ENSG00000239899	Chromatin interaction
ENSG00000162976	Chromatin interaction
ENSG00000196208	Chromatin interaction
ENSG00000143870	Chromatin interaction
ENSG00000264010	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10166950	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10166997	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs10495579	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11676318	0.90[EUR][1000 genomes]
rs11681385	0.90[EUR][1000 genomes]
rs13392854	0.90[EUR][1000 genomes]
rs2357991	0.93[EUR][1000 genomes]
rs28433865	0.90[EUR][1000 genomes]
rs55935965	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72785428	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72785429	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520789	chr2:11259067-11312224	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11269800-11274000	Enhancers	Fetal Brain Male	brain
2	chr2:11270600-11273200	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr2:11271400-11273200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:11271400-11274200	Active TSS	Brain Anterior Caudate	brain
5	chr2:11271800-11273200	Active TSS	Brain Hippocampus Middle	brain
6	chr2:11271800-11273600	Active TSS	Brain Cingulate Gyrus	brain
7	chr2:11272200-11273200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:11272400-11273400	Enhancers	Spleen	Spleen
9	chr2:11272400-11273600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
10	chr2:11272400-11273600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr2:11272400-11273600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr2:11272400-11274000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:11272600-11273200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:11272600-11273400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr2:11272600-11273400	Active TSS	Fetal Brain Female	brain
16	chr2:11272600-11273400	Flanking Active TSS	Fetal Thymus	thymus
17	chr2:11272600-11273400	Flanking Active TSS	Dnd41	blood
18	chr2:11272600-11273600	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr2:11272600-11273600	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr2:11272600-11273600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr2:11272600-11273600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr2:11272600-11273600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
23	chr2:11272600-11273600	Flanking Active TSS	Hela-S3	cervix
24	chr2:11272600-11273800	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr2:11272600-11273800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:11272600-11273800	Flanking Active TSS	Colonic Mucosa	Colon
27	chr2:11272800-11273200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:11272800-11273200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:11272800-11273200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:11272800-11273200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:11272800-11273200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:11272800-11273200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:11272800-11273200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr2:11272800-11273200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr2:11272800-11273200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:11272800-11273200	Active TSS	Muscle Satellite Cultured Cells	--
37	chr2:11272800-11273200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:11272800-11273200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:11272800-11273200	Active TSS	Liver	Liver
40	chr2:11272800-11273200	Active TSS	Brain Germinal Matrix	brain
41	chr2:11272800-11273200	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr2:11272800-11273200	Active TSS	Rectal Mucosa Donor 31	rectum
43	chr2:11272800-11273200	Active TSS	Right Ventricle	heart
44	chr2:11272800-11273200	Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr2:11272800-11273200	Bivalent/Poised TSS	HepG2	liver
46	chr2:11272800-11273200	Active TSS	HSMM	muscle
47	chr2:11272800-11273200	Active TSS	HUVEC	blood vessel
48	chr2:11272800-11273200	Active TSS	K562	blood
49	chr2:11272800-11273200	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
50	chr2:11272800-11273200	Active TSS	NH-A	brain

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